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Resolving the taxonomic ambiguities in the distribution of Acropoma splendens (Lloyd, 1909) from Arabian Sea of Indian EEZ: An integrative taxonomic approach

International Journal of Advanced Biochemistry Research · 2024 · Vol. 8(7S) · pp. 837–846
Sugumar Ramkumar✉Grishma Sharad PatilV D MhatreP A KhandagaleU H RaneBhagyalakshmi KalidassL RanjithVaibhav Milan TawdeMukunda GoswamiW. S. Lakra

Abstract

Seventy-three specimens of Acropomatids measuring 40.7-90.8 mm standard length were collected from commercial multi-day fishing trawlers at 25-50 m depth off the Mumbai coast, Arabian Sea, Northwest coast of India. The morphological and morphometric diagnostic characters of the collected specimens matches with Acropoma splendens (Lloyd, 1909) with the key features viz., the presence of a vertical line on the cheek, four rows of scales between the first dorsal fin and lateral line; gill raker count 19 – 22 numbers; pectoral fin rays 16 numbers; anus situated closer to the pelvic fin than to the anal fin; short and U-shaped luminous gland around the anus with a length of 12 – 16.9 % of standard length. Further, through cytochrome c oxidase subunit I (COI) gene sequencing analysis validated and confirmed the identity of the specimens as Acropoma splendens (Lloyd 1909). The comparison of COI gene sequences of A. splendens in the present study with the COI gene sequences of its interspecies of the Acropoma genus revealed that Acropoma splendens had the highest intraspecies distance (5.8) with A. japonicum and the least intraspecies distance (1.839) with A. hanedai and A. argentistigma was 3.0. Thus, integrative taxonomic unraveling the taxonomic ambiguity of the species and confirmed the presence of A. splendens for the first time from the Arabian Sea of Indian Exclusive Economic Zone (EEZ).

Full Text

Tables and figures are in the full-text PDF.

Introduction

Laternbelly of the family Acropomatidae, representing the genus Acropoma Temminck and Schlegel 1843, has 12 valid species (Okamoto et al., 2021) [27] with global distribution in the Indo-Pacific region from Vanuatu to South Africa (Okamoto and [25,28,27] . The species includes A. japonicum Günther, 1859 Glowbelly, A. splendens (Lloyd 1909) Indian lanternbelly, A. hanedai Matsubara 1953 [12,21,11,2,26,42,43,29,9] . The location, shape, and length of the luminous gland, shape of the proximal radial of the 1st anal-fin spine pterygiophore, gill raker count, number of scales between the lateral line and 1 st dorsal-fin base, presence/absence of cycloid scales, and vertical line on the cheek are the most important diagnostic characters for species differentiation in the genus Acropoma (Katayama 1959 [15,42,43,25,27] . A. splendens was first discovered in the Gulf of Oman in 1909 as Synagrops splendens by Llyod. In the Arabian Sea, this species has been misreported as Acropoma japonicum by many authors (Fowler 1927 [7,24,17,13,1,3,20,14,31] until 2016, when Okamoto and Golani described this as a new species as Acropoma lacrima in 2017 based on paratypes from the northwest coast of India, but later confirmed it as a junior synonym of A. splendens (Okamoto et al. 2021; Prokofiev 2019) [27,30] . In the Indian EEZ, A. splendens were misidentified as A. japonicum by Balachandran and Nizar in the year 1990 [1] from the specimen caught in the Arabian Sea at the depth 140 m by operating bottom trawl net in the Fishery Oceanographic Research Vessel (FORV), Sagar Sampada (Location: Latitude 11°29'N Longitude 74°30'E). Another misidentified report of A. splendens by Fowler (1927) [7] from Bombay (currently Mumbai) waters of the Arabian Sea was A. japonicum. Another misidentified report of A. splendens as A. argentistigma from the Bay of Bengal region of the Indian EEZ, based on specimens collected from the Mohana, Digha, Fish markets on the West Bengal coast without confirming the gill raker count, pectoral fin ray count, and dark vertical line mark on the cheek in the preserved specimen (Yennawar et al., 2012) [44] . The aim of this study was to resolve the taxonomic ambiguity of this species, A. splendens, and to validate the presence of A. splendens in the Indian EEZ through an integrative taxonomic approach. This study also confirmed species identification by comparing the sequences of closely related species of the Acropoma genus available globally.

Materials and Methods

Sample collection information

Acropoma samples were collected from trawl bycatch landings at the New Ferry Wharf fish landing centre caught off the Mumbai coast, Arabian Sea, Northwest coast of India at a depth range of 25-50 m (Figure 1). The coloration and pigmentation of the fresh specimens were recorded and photographed at the landing centre. A total of 73 specimens of A. splendens were brought to the laboratory of the Mumbai Regional Station of ICAR-CMFRI, Mumbai, for further analysis. Of the 73 specimens analysed, 34 specimens were collected in January 2018, 4 specimens were collected in January 2021, and the remaining 35 specimens were collected in January 2023 from the Multiday trawl fish landings at the New Ferry Wharf fish landing centre. The present study collected 73 A. splendens specimens from the heaps of trash fish landings at the New Ferry Wharf fish landing centre, Mumbai, as a component of the trash fish commodity. These trawlers regularly catch A. splendens as bycatch, targeting species such as ribbon fish, bombay duck, gold-spotted grenadier anchovy, sciaenids, and marine ariids from September to January annually. Typically, these trawlers bring their bycatch from the last four hauls of the trip as trash fish heaps during the peak fishing season, which runs from September to November. During the lean season, trash fish landings dominated the total catch composition compared with the targeted fish catch by these trawlers, usually from December to March every year. The landing centre price of these trash fish ranged from 15 to 28 INR per kilogram. Fishmeal plants use the trash fish landings as raw materials. The trawl fishery landings in the New Ferry wharf fish landing centre on the Mumbai coast discard 42.19 % of their bycatch at sea, which amounts to 33.25 % of the total catch annually, including juveniles of commercially important fishes that have huge economic potential in domestic markets (Ramkumar et al., 2019; Sugumar et al., 2015, 2016) [35,37,36] . Trash fishes constitute the constituents of the bycatch in the multiday trawl fishery of the Mumbai coast as low-value bycatch (LVB) commodities.

Sample analysis

Morphometric measurements and meristics counts were performed using the methods described by Okamoto (2014) [29] . All morphometric measurements were performed using a digital caliper to the nearest 0.1 mm and were expressed as proportions of standard length (% of SL) (Table 1). For molecular identification and characterization of the specimens, muscle tissue from four fish samples collected in January 2021 was aseptically removed and stored at -20°C in absolute alcohol. The specimens were stored at the Mumbai Regional Station of the ICAR-CMFRI, Mumbai. Gastro Somatic Index (GaSI) and Gonado Somatic Index (GSI) for A. splendens were estimated using methods described by De Silva and Anderson (1995) [4] . The maturity stages of A. splendens were determined using methods described by Nikolsky (1963) [23] . A single spine between the first and second dorsal fins was counted as the dorsal fin spine according to Okamoto and Ida (2002) [26] . The rudimentary gill raker count was combined with the gill raker count. Species identification was performed using the key diagnostic characteristics of A. splendens as reported by Okamoto and Golani (2017) [25] , Okamoto et al. (2021) [27] , and Lloyd (1909) [18] . SL represents the short form of the standard length.

Genomic DNA isolation, amplification and sequencing

DNA was extracted from the muscle tissue of A. splendens collected in January 2021 using the CTAB method (Mishra, 2019) [22] . The purity and concentration of the DNA were determined using a spectrophotometer (NanoDrop Thermo Fisher Scientific, USA). Utilizing the cytochrome c oxidase subunit I (COI) gene universal primers (Table 2), a 655 bp region from the 5' end of the gene was amplified. PCR amplification was performed using a C1000 thermal cycler (Bio-Rad Laboratories). The optimized PCR cycles consisted of an initial denaturation at 94°C for 3 min, followed by 29 cycles of 30sec denaturation at 94°C, 30sec annealing at 54°C, 1 min extension at 72°C, and a final extension at 72°C for 7 min. The amplified PCR products were purified using the GeneJet PCR Clean Up Kit (Thermo Fisher Scientific, USA) following the manufacturer's protocol. The PCR-amplified products were visualized on a 1.5 % agarose gel and viewed using a Gel Documentation System (Bio-Rad Laboratories, USA). After purification, the samples were sent to Macrogen (Seoul, Korea) for sequencing.

Sequence analysis

The sequences obtained were aligned using ClustalW (Thompson et al., 2002) [38] in MEGA7 (MEGA7: Molecular Evolutionary Genetics Analysis version 7.0) for larger datasets (Sudhir et al., 2015) [34] . The aligned sequences were then passed through (National Center for Biotechnology Information) ORF finder (https://www.ncbi.nlm.nih.gov/orffinder/) to obtain the coding sequences. The coding sequences were subsequently searched using the BLAST nucleotide database (https://blast.ncbi.nlm.nih.gov/Blast.cgi) to confirm the gene. Pairwise distances were calculated based on the pdistance using MEGA7. Based on the pairwise distances calculated using the COI sequences, a neighbor-joining (NJ) tree with a bootstrap value of 1000 (Kimura 1980) [16] was constructed. The sequences were then submitted to GenBank, and accession numbers were obtained, the details of which are given in Table 3.

Results and Discussions Systematic Position:

Order: Acropomatiformes Family: Acropomatidae Species: Acropoma splendens (Lloyd, 1909). English name: Indian lanternbelly Fresh and alcohol-preserved specimens of Acropoma splendens collected in this study are shown in Figures 2 and3a, respectively.

Identification character diagnosed

Body laterally compressed with greatest depth in the anterior part of the first dorsal fin. The head length is nearly half of the standard length, and its proportion to SL is 33.9-51.5 % SL. The head and eyes are larger in size. The eye orbit rim is slightly elevated above the upper contour of the head. A large mouth opening with the maxilla extending below the middle of the eye. Palatines and vomers with villiform teeth. Conical teeth observed in the upper and lower jaws. The symphysis of the lower jaw did not protrude. Scales are large and mostly ctenoid, and some ctenoid scales have less or meager serrations at the end. Caudal peduncle covered with ctenoid scales. Few cycloid scales were observed in the lower middle part of the body. Four rows of scales descended from the base of the first dorsal fin to the lateral line (Figure 4). Two dorsal fins were also observed. There are eight spines on the dorsal fin, and the last spine lacking a connection with any of the fin membranes. Anal-fin with three spines and seven rays were noticed. The anus was positioned closer to the pelvic fin than the anal fin. Caudal-tail is forked. Gill rakers are slender, with rudimentary buds at the ends of both the upper and lower limbs. The total gill raker count is 19 -22 in numbers. The luminous gland was short and U-shaped around the anus (Figure 5a). The luminous gland is Ushaped, and its length is proportional to the standard length (SL) ranges from 12-16.9 % SL. The standard length (SL) of the 73 A. splendens specimens range from 40.7 mm -90.8 mm. The preserved specimen showed a vertical line on the cheek. The pectoral fin ray counts were 16. A concavity was observed on the anterior surface of the proximal radial anal fin pterygiophore. The comparative morphometric scale and meristic counts of the present study and earlier records are presented in Table [17,3,14,5] , Gulf of Oman (Llyod 1909; Norman 1939) [18,24] , Gulf of Aden (Heemstra 1984) [13] , Mumbai coast of the Arabian Sea (Okamoto and Golani 2017; present study) [25] , Arabian Sea (Balachandran and Okamoto and Golani 2017) [1,3,20,31,25] , Bay of Bengal (Yennawar et al., 2012) [44] , Myanmar (Psomadakis et al., 2019) [32] , and Andaman Sea off southwestern Thailand (Okamoto et al., 2021) [27] .

Coloration

The fresh specimen was pinkish in color. The operculum, ventral part, and mid-portion of the body are silvery-white. All the fins were slightly pinkish. The ventral side of the body, as well as the pelvic and anal fins, displayed melanophores. The alcohol-preserved specimen displays a dark black vertical line on the cheek (Figure 3b). The luminous gland was yellow-colored in fresh condition (Figure 5b).

Synonym of A. splendens

Lloyd in 1909 originally described A. splendens as Synagrops splendens from the Gulf of Oman as a holotype. In 2017, Okamoto and Golani described a specimen from Bombay (currently Mumbai) coast of the Arabian Sea as a new species, Acropoma lacrima sp. nov., previously misidentified as A. japonicum in other studies (Fowler 1927; Kotthaus 1974; Balachandran and Nizar 1990) [7,17,1] . Similarly, Yennawar et al. (2012) [44] misidentified A. splendens in the Bay of Bengal as A. argentistigma and it was re-identified by Okamoto and Golani (2017) [25] as A. splendens, based on morphometric measurements, meristic counts, and photo information obtained from Yennawar. Prokofiev (2019) [30] argued that A. lacrima Okamoto and Golani (2017) are synonymous with A. splendens (Llyod, 1909). Okamoto et al., 2021 also mentioned that the Acropoma species recorded from the Arabian Sea and Bay of Bengal in Indian waters is A. splendens, while reporting its distribution off southwestern Thailand for the first time. Further, Makoto Okamoto, in personal communication with the first author of this present study, stated that Acropoma lacrima is a junior synonym of A. splendens. Similarly, the fishbase website mentioned that Synagrops splendens Lloyd, 1909 is a senior synonym of A. splendens and Acropoma lacrima Okamoto & Golani, 2017 is a junior synonym of Acropoma splendens (Lloyd, 1909), and the accepted name is Acropoma splendens (Lloyd, 1909). Hence, the GenBank accession number of the four specimens of A. lacrima in the present study was read as A. splendens COI sequences for future comparison globally.

Comparison

Among Acropoma species, a vertical line on the cheek was observed in A. splendens and A. hanedai. However, A. splendens was easily distinguished from A. hanedai by its U-shaped luminous gland (vs. elongated) and anus nearer to pelvic-fin origin (vs. anus halfway between pelvic-fin and anal-fin origin) (Okamoto & Golani 2017 [25] ; Okamoto et al., 2021 [27] ; in the present study, the same observation was observed for A. splendens in the case of the luminous gland). The U-shaped Luminous gland has similar characteristics to those of A. splendens and A. argentistigma, but these species can be easily differentiated with a gill rakers count is 19-24 [25,27] . The present study also recorded 19-22 numbers of gill rakers and 16 pectoral fin rays consistent with earlier reports on A. splendens. A. japonicum has a U-shaped luminous gland and more than 20 gill rakers, such as in A. splendens, but lacks cycloid scales on the lateral side of the body vs. weakly cycloid and ctenoid scales in A. splendens (Okamoto & Golani 2017; Okamoto et al., 2021) [25,27] . In the present study, cycloid scales were also observed on the mid-lateral side of the body, and weak ctenoid scales were observed throughout the body. Present study presenting the wider range of SL of A. splendens (SL = 40.7 -90.8 mm) than the earlier records which is mainly due to the larger sample size (n=73) vs. Okamoto et al. 2021 [27] (n=5) vs. Okamoto and Golani 2017 [25] (n=6) vs. Yennawar et al. 2012 [44] (n=30). Therefore, the present study has opened up an avenue worldwide to understand new variations in the morphometric measurements of A. splendens. The present study recorded the smallest SL (40.7 mm) for A. splendens, whereas Yennawar et al. (2012) [44] recorded the highest SL (110 mm) for A. splendens. To date, the known SL range for A. splendens is 40.7 -110 mm. Luminous gland length in this study ranged from 12 -16.9 % SL (vs. 15.6-17.6 % SL in Okamoto et al. 2021 [27] ; 15 -16 % in Okamoto and Golani 2017) [25] . The wider variation in the present study is mainly due to the inclusion of smaller-sized A. splendens specimens, which were not covered in previous studies. Counts of pectoral-fin rays (15 nos.) and gill rakers (17-18 nos.) of A. splendens reported by Yennawar et al. (2012) [44] (Table 1) is not matching with accepted diagnostic characters of A. splendens but Okamoto and Golani 2017 [25] mentioned that with confirmation of vertical line on the cheek as well as 16 numbers of pectoral-fin rays through personal communication with Yennawar results in the reidentification of A. argentistigma of Bay of Bengal as A. splendens. Except for these two meristic counts, all other counts as well as morphometric measurements of Yennawar et al. (2012) [44] matched with identification characteristics of A. splendens of the present study.

Biological observations

The Gastro somatic index (GaSI) helps in determining the feeding conditions of fish. In present study it ranged between 0.61 to 5.89 with an average of 2.47. The major food item was Acetes spp., followed by fish bones, scales, and digested matter. Gut content analysis showed that A. splendens is a carnivorous species. The gonadosomatic index (GSI) was used to determine the stage of ovarian maturation and the degree of ripeness. It was observed between 0.69 to 3.14 with a mean of 1.82 in the present study. Of the observed females, 46.66 % were mature, 36.66 % were mature or spent, and 16.66 % were immature. This shows that A. splendens is a continuous batch spawner that may result in the release of a cohort every month owing to the availability of its food year-round. The overall sex ratio (male:female) for the 73 specimens was 1:7.5, and the dominance of female specimens was observed.

COI Gene sequencing and analyses of Acropoma lacrima

Sequence alignment of the four Acropoma lacrima individuals yielded a nucleotide base pair ranging from 629 to 640 base pairs and their nucleotide composition is mentioned in Table 3. The Maximum Composite Likelihood (MCL) estimate for nucleotide substitution (Table 4) shows the probability of nucleotide substitution (r) from one base (row) to another base (column). All values are expressed in a tabulated form, where entries within a row should be compared. The rates of different transitional substitutions are shown in bold and those of transversional substitutions are shown in italics. The overall transition/transversion bias is 0.437.

Genetic distance

A comparison of the four Acropoma lacrima individuals (Al1, Al2, Al3, and Al4) based on COI gene sequences was performed to determine the distances within the same species, and the details are listed in Table 5. The lowest genetic distance of 0.000 was found between Al4 and Al3, whereas the maximum genetic distance of 2.000 was found between Al3 and Al2. The pairwise distances among the different species in the Acropoma genus for which nucleotide data were available in the NCBI database were determined using the p-distance model (Table 6). Acropoma lacrima had the highest intraspecies distance (5.8) with Acropoma japonicum and the least intraspecies distance (1.839) with Acropoma hanedai.

Evolutionary relationships using phylogenetic tree

With the help of phylogenetic analysis, it has become easier to identify the most accurate evolutionary relationships among organisms and the distances between nucleotide sequences. In this study, a phylogenetic tree was generated for Acropoma lacrima individuals (Figure 6) using the neighbor-joining (NJ) method (Saitou and Nei 1987) [33] in MEGA 7. For the NJ tree, evolutionary distances were computed using the Kimura 2-parameter method and expressed in units of number of base substitutions per site. In addition, a similar NJ method-based phylogenetic tree (Figure 7) using Kimura 2-parameter was constructed for intraspecies individuals. For this purpose, Acropoma japonicum, Acropoma hanedai, and Acropoma argentistigma were used as outgroups to understand the evolutionary relationships among different species of the Genus Acropoma. The outgroup sequences were obtained from NCBI and their accession numbers are listed in Table 6. This study is the first to provide COI gene sequences of Acropoma lacrima and A. splendens. The COI gene has been used as a DNA barcode because of its high interspecies variation, low intraspecies variation, and universality of priming sites for large taxonomic groups (Folmer et al., 1994) [6] . The mutation rate in the COI gene is fast enough to differentiate closely related species and conspecifics owing to conserved sequences (Ha et al., 2018) [10] . COI offers a high level of diversity that can be used to understand the relationships between closely related species or estimate phylogeographic groupings within species (Luo et al., 2011; Wares et al., 2001; Trontelj et al., 2005) [19,41,39] .

Acknowledgments

We acknowledge the ICAR-CMFRI Mumbai Regional Station and Director, ICAR-CMFRI, for their support in providing access to funds for sampling and lab facility utilization.

Conclusion

The present study provides a holistic picture of the morphometric variation of A. splendens collected from the Arabian Sea off the Mumbai coast. The current study has also provided the sex ratio, GaSI, GSI, and food preference of A. splendens for the first time in Indian waters. This study also confirmed that A. splendens is distinct from its closely related species through comparative sequencing analyses of the COI gene of Acropoma lacrima (junior synonym of A. splendens) with A. japonicum, A. argentistigma, and A. hanedai obtained from the NCBI nucleotide database. Hence, the Acropoma species on the Mumbai coast of the Arabian Sea was validated as Acropoma splendens (Llyod, 1909). Thus, integrative taxonomic resolving the taxonomic ambiguity of the species and confirmed the presence of A.

splendens for the first time from the Arabian Sea of Indian EEZ.

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Citations
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field-weighted impact
References
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Percentile
11%
vs. same field & year
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